Recently, I hit a wierdness in a JIRA filter that did not return all issues I expected. After some testing and dialog with Atlassian - in short - a bug report was created and shortly closed by Atlassian with the comment:
This kind of behaviour is present for multiple JQL cases e.g. custom fields, labels, projects and is an expected, designed behaviour hence this issue will not be considered a bug.
Pawel, Jira Developer
In short, this is regarding customefields (etc) that can be empty (as having a null value in the database) - typically represented as "none" is a select filed.
To sum up, if You are searching a project and You JQL has some "not in" or "!=" operation, be sure to add a phrase for EMPTY:
will return all issues, where as
needs to be written as
to actually show all issues.
So It seems for every negation on fields and labels etc in Your JQL, EMPTY need to be taken in account also.